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Conserved domains on  [gi|6323164|ref|NP_013236|]
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Slx4p [Saccharomyces cerevisiae S288C]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SLX4_RIM2 cd22869
second RIM (Rtt107 interaction motif) of Saccharomyces cerevisiae structure-specific ...
 535-587 8.15e-22

second RIM (Rtt107 interaction motif) of Saccharomyces cerevisiae structure-specific endonuclease subunit SLX4 and similar proteins; SLX4 is the regulatory subunit that interacts with and increases the activity of different structure-specific endonucleases. It plays distinct roles in protecting genome stability by resolving diverse forms of deleterious DNA structures. SLX4 has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ssDNA. It is critical in maintaining the integrity of the ribosomal DNA (rDNA) loci, where it has a role in re-starting stalled replication forks. It also has Holliday junction resolvase activity in vitro. It interacts with the structure-specific RAD1-RAD10 endonuclease and promotes RAD1-RAD10-dependent 3'-non-homologous tail removal (NHTR) during repair of double-strand breaks by single-strand annealing. SLX4 also promotes recovery from DNA-alkylation-induced replisome stalling during DNA replication by facilitating the error-free mode of lesion bypass. This does not require SLX1 or RAD1-RAD10, but probably regulator of TY1 transposition protein 107 (Rtt107). SLX4 contains two Rtt107 interaction motif (RIM) regions, which are referred to as RIM1 and RIM2, respectively. This model corresponds to the second RIM region.


:

Pssm-ID: 439372  Cd Length: 53  Bit Score: 89.12  E-value: 8.15e-22
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 6323164  535 GSSIRVKLLQESVVKLNPKLVKHNFYRVEANDSEEEETEFDDQFCIADIQLVD 587
Cdd:cd22869   1 GSSIRVKLLQESVVKLNPKLVKHNCYRVEANDSEEEETEFDDQFCIADIQLVD 53
Slx4 pfam09494
Slx4 endonuclease; The Slx4 protein is a heteromeric structure-specific endonuclease found ...
 685-745 2.16e-18

Slx4 endonuclease; The Slx4 protein is a heteromeric structure-specific endonuclease found from fungi to mammals. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates.


:

Pssm-ID: 430644  Cd Length: 60  Bit Score: 79.47  E-value: 2.16e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6323164    685 FDHLTELIEAFPDFLERIYTFEPIPLNELIEKLFSAEpFVSQIDEMTIREWADVQGICLRN 745
Cdd:pfam09494   1 FEAITELIKSDPSLYEKILTYEPIVLEDLTAWLNEGG-FLIEVDPGTLKEWCDSQGICFTN 60
PLN02698 super family cl31922
Probable pectinesterase/pectinesterase inhibitor
 585-692 2.20e-03

Probable pectinesterase/pectinesterase inhibitor


The actual alignment was detected with superfamily member PLN02698:

Pssm-ID: 178301 [Multi-domain]  Cd Length: 497  Bit Score: 41.08  E-value: 2.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323164   585 LVDSSKISTKDSTQNPTTSNDIIDTSAASSIASPEKFCEIMMSQSMKELRQSLKTVGLKPMRTKVEiIQSLQTASQILST 664
Cdd:PLN02698  56 LVNKTISETNLPLSSSMGSSYQLSLEEATYTPSVSDSCERLMKMSLKRLRQSLLALKGSSRKNKHD-IQTWLSAALTFQQ 134

                         90       100       110
                 ....*....|....*....|....*....|..
gi 6323164   665 ANPDNKGEHGGVANFSKI----EIFDHLTELI 692
Cdd:PLN02698 135 ACKDSIVDSTGYSGTSAIsqisQKMDHLSRLV 166
 
Name Accession Description Interval E-value
SLX4_RIM2 cd22869
second RIM (Rtt107 interaction motif) of Saccharomyces cerevisiae structure-specific ...
 535-587 8.15e-22

second RIM (Rtt107 interaction motif) of Saccharomyces cerevisiae structure-specific endonuclease subunit SLX4 and similar proteins; SLX4 is the regulatory subunit that interacts with and increases the activity of different structure-specific endonucleases. It plays distinct roles in protecting genome stability by resolving diverse forms of deleterious DNA structures. SLX4 has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ssDNA. It is critical in maintaining the integrity of the ribosomal DNA (rDNA) loci, where it has a role in re-starting stalled replication forks. It also has Holliday junction resolvase activity in vitro. It interacts with the structure-specific RAD1-RAD10 endonuclease and promotes RAD1-RAD10-dependent 3'-non-homologous tail removal (NHTR) during repair of double-strand breaks by single-strand annealing. SLX4 also promotes recovery from DNA-alkylation-induced replisome stalling during DNA replication by facilitating the error-free mode of lesion bypass. This does not require SLX1 or RAD1-RAD10, but probably regulator of TY1 transposition protein 107 (Rtt107). SLX4 contains two Rtt107 interaction motif (RIM) regions, which are referred to as RIM1 and RIM2, respectively. This model corresponds to the second RIM region.


Pssm-ID: 439372  Cd Length: 53  Bit Score: 89.12  E-value: 8.15e-22
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 6323164  535 GSSIRVKLLQESVVKLNPKLVKHNFYRVEANDSEEEETEFDDQFCIADIQLVD 587
Cdd:cd22869   1 GSSIRVKLLQESVVKLNPKLVKHNCYRVEANDSEEEETEFDDQFCIADIQLVD 53
Slx4 pfam09494
Slx4 endonuclease; The Slx4 protein is a heteromeric structure-specific endonuclease found ...
 685-745 2.16e-18

Slx4 endonuclease; The Slx4 protein is a heteromeric structure-specific endonuclease found from fungi to mammals. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates.


Pssm-ID: 430644  Cd Length: 60  Bit Score: 79.47  E-value: 2.16e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6323164    685 FDHLTELIEAFPDFLERIYTFEPIPLNELIEKLFSAEpFVSQIDEMTIREWADVQGICLRN 745
Cdd:pfam09494   1 FEAITELIKSDPSLYEKILTYEPIVLEDLTAWLNEGG-FLIEVDPGTLKEWCDSQGICFTN 60
PLN02698 PLN02698
Probable pectinesterase/pectinesterase inhibitor
 585-692 2.20e-03

Probable pectinesterase/pectinesterase inhibitor


Pssm-ID: 178301 [Multi-domain]  Cd Length: 497  Bit Score: 41.08  E-value: 2.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323164   585 LVDSSKISTKDSTQNPTTSNDIIDTSAASSIASPEKFCEIMMSQSMKELRQSLKTVGLKPMRTKVEiIQSLQTASQILST 664
Cdd:PLN02698  56 LVNKTISETNLPLSSSMGSSYQLSLEEATYTPSVSDSCERLMKMSLKRLRQSLLALKGSSRKNKHD-IQTWLSAALTFQQ 134

                         90       100       110
                 ....*....|....*....|....*....|..
gi 6323164   665 ANPDNKGEHGGVANFSKI----EIFDHLTELI 692
Cdd:PLN02698 135 ACKDSIVDSTGYSGTSAIsqisQKMDHLSRLV 166
 
Name Accession Description Interval E-value
SLX4_RIM2 cd22869
second RIM (Rtt107 interaction motif) of Saccharomyces cerevisiae structure-specific ...
 535-587 8.15e-22

second RIM (Rtt107 interaction motif) of Saccharomyces cerevisiae structure-specific endonuclease subunit SLX4 and similar proteins; SLX4 is the regulatory subunit that interacts with and increases the activity of different structure-specific endonucleases. It plays distinct roles in protecting genome stability by resolving diverse forms of deleterious DNA structures. SLX4 has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ssDNA. It is critical in maintaining the integrity of the ribosomal DNA (rDNA) loci, where it has a role in re-starting stalled replication forks. It also has Holliday junction resolvase activity in vitro. It interacts with the structure-specific RAD1-RAD10 endonuclease and promotes RAD1-RAD10-dependent 3'-non-homologous tail removal (NHTR) during repair of double-strand breaks by single-strand annealing. SLX4 also promotes recovery from DNA-alkylation-induced replisome stalling during DNA replication by facilitating the error-free mode of lesion bypass. This does not require SLX1 or RAD1-RAD10, but probably regulator of TY1 transposition protein 107 (Rtt107). SLX4 contains two Rtt107 interaction motif (RIM) regions, which are referred to as RIM1 and RIM2, respectively. This model corresponds to the second RIM region.


Pssm-ID: 439372  Cd Length: 53  Bit Score: 89.12  E-value: 8.15e-22
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 6323164  535 GSSIRVKLLQESVVKLNPKLVKHNFYRVEANDSEEEETEFDDQFCIADIQLVD 587
Cdd:cd22869   1 GSSIRVKLLQESVVKLNPKLVKHNCYRVEANDSEEEETEFDDQFCIADIQLVD 53
Slx4 pfam09494
Slx4 endonuclease; The Slx4 protein is a heteromeric structure-specific endonuclease found ...
 685-745 2.16e-18

Slx4 endonuclease; The Slx4 protein is a heteromeric structure-specific endonuclease found from fungi to mammals. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates.


Pssm-ID: 430644  Cd Length: 60  Bit Score: 79.47  E-value: 2.16e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6323164    685 FDHLTELIEAFPDFLERIYTFEPIPLNELIEKLFSAEpFVSQIDEMTIREWADVQGICLRN 745
Cdd:pfam09494   1 FEAITELIKSDPSLYEKILTYEPIVLEDLTAWLNEGG-FLIEVDPGTLKEWCDSQGICFTN 60
PLN02698 PLN02698
Probable pectinesterase/pectinesterase inhibitor
 585-692 2.20e-03

Probable pectinesterase/pectinesterase inhibitor


Pssm-ID: 178301 [Multi-domain]  Cd Length: 497  Bit Score: 41.08  E-value: 2.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323164   585 LVDSSKISTKDSTQNPTTSNDIIDTSAASSIASPEKFCEIMMSQSMKELRQSLKTVGLKPMRTKVEiIQSLQTASQILST 664
Cdd:PLN02698  56 LVNKTISETNLPLSSSMGSSYQLSLEEATYTPSVSDSCERLMKMSLKRLRQSLLALKGSSRKNKHD-IQTWLSAALTFQQ 134

                         90       100       110
                 ....*....|....*....|....*....|..
gi 6323164   665 ANPDNKGEHGGVANFSKI----EIFDHLTELI 692
Cdd:PLN02698 135 ACKDSIVDSTGYSGTSAIsqisQKMDHLSRLV 166
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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